I am a novice at PERL and came across a script to sort sequences in a
mulitple sequence fasta file by name. It does what it should. However, it
does give the following error:
"Replacement list is longer than search list at
C:/Perl/site/lib/Bio/Range.pm line 251."
I'm not too worried about this as it does work.
I have another PERL script that takes uniprotkb fasta headers and trims
them to just the organism name and strain. I would like to run this script
and the sorting script together on a series of files and then concatenate
the results. I can run the scripts separately and they work. I tried to
put my trimming script before the sorting script in a single script, and it
no longer works.
Could anyone take a look and see if there is something simple I am doing
wrong? Or, is there a better way to do this? I will need to do this
repetitively on batches of 33 files. I am running PERL 5.12.2 on Windows XP
sp3 with BioPerl 1.6.1.
Attached:
L1.fasta - example Uniprot file to be trimmed and sorted
L1ss.fasta - desired output from running the scripts in sequence
fastaSortByName.pl - script from Naoki Takebayashi
(http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl-scripts/perl-scripts.html)
shortenIDs.pl - my fasta header trimming script
shortsort.pl - my attempt at merging the two scripts above into a single
one